Oh, I think she loves it when we find all the connections and when it makes her look like a much better writer than she actually is. She can pretend that she meant all the clever stuff and it's not just all of us filling in her massive plot holes.
Jamie and Claire are going by Fraser on the Artemis, but when the Porpoise comes along he thinks that it will be safer if they are Malcolm. Jamie Fraser is much too recognisable a name for the English, especially coupled with his height and red hair. In Edinburgh, he was Malcolm for printing, Jamie Ruaidh for smuggling and only Fraser at home. he was trying so hard to keep all the strands of his life separate and to keep everyone safe from the repercussions of his activities.
He took back his name in Georgia because he felt that it was safe to do so. The English military presence had been, I think, scaled back in America by that time, obviously before the revolution kicked off. No-one from Edinburgh was likely to be around to recognise him and loads of Scots turned up in the states all the time. There was, in the book, talk of them settling on Eleutheria or another caribbean island not under English control but, even then, he might not have been able to go by his real name.
Fergus's naming ties in with the whole idea o identity which suffuses the book. Jamie is able to finally give Fergus his name, openly and safely, among friends, confirming his own identity and Fergus's. Unlike when he claimed Willie in secrecy because of the danger to himself and the effect that would have had on the child. Tears tae a gless e'e.